RRP8 RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12
idx	1113	1188	1114	1189
TRCN#_or_BGC#	BGC#0000831	BGC#0000820	BGC#0000831	BGC#0000820
shRNA_or_gRNA_sequence	GATTACGGGCCCAAGGCCCG	CTCGAAATGCAGAACGACGC	GATTACGGGCCCAAGGCCCG	CTCGAAATGCAGAACGACGC
PAM	CGG	CGG	CGG	CGG
Name	RRP8_92	RPS21_82	RRP8_92	RPS21_82
Sample_ID	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	RRP8	RPS21	RRP8	RPS21
qPCR_result		75.2		54.4
Ave_qPCR		64.8
RT-qPCR_primer-F		catccatccagatgaacgtg
RT-qPCR_primer-R		ccccgcagatagcataagtt
protein_conc	396	1744	482	1679
WB_result	79.3	53.4	83.0	62.9
Ave_WB	81.2	58.2
WB_DONE_date	2/4/22	3/10/22
MW	51KD	9.1kd
IP
antibody_Cat#	A304-202A	A305-070A	LOT #1	LOT #1
Antibody DCC ID		NO ID		8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5253	5328	5254	5329

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS21	Product_ID: A305-070A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS21-human

Experiment Status

	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12
Sample_ID	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12
Sample Name
Sample Name	RPS21-BGKcLV33-11		RPS21-BGKcLV33-12
RBP	RPS21	RRP8	RPS21	RRP8
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10641	10697	10642	10698

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-11	BGKcLV33-12
Sample #	11	12
Sample Name	RPS21-BGKcLV33-11	RPS21-BGKcLV33-12
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	297	298
Peak_Molarity	63.30	64.50
libSampleQC_DNA_Well	DNA_Library_set53/set1/C6.png	DNA_Library_set53/set1/D6.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set53/set1/C2.png	RNA_Library_set53/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-11	BGKcLV33-12
RBP	RPS21	RPS21
Batch_ID	BGKcLV33	BGKcLV33
WB_result	53.400	62.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3272	3273

Sequencing Information

	BGKcLV33-11	BGKcLV33-12
Sample_ID	BGKcLV33-11	BGKcLV33-12
Sample Name	RPS21-BGKcLV33-11	RPS21-BGKcLV33-12
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	101,841,958	97,473,102
total_aligned_reads	89,076,560	88,646,350
unique_aligned_reads	81,483,480	81,174,234
percent_uniqueAligned	0.80010	0.83279
correlation_replicates	0.993840	0.993840
spikein_reads	18,910	9,296
percent_spikeins	0.00019	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2039	2040

Data Submission Information

	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12	BGKcLV33-12	BGKcLV33-12
ENCODE_alias	brenton-graveley:RPS21-BGKcLV33	brenton-graveley:RPS21-BGKcLV33-11	brenton-graveley:L-RPS21-BGKcLV33-11	brenton-graveley:RPS21-BGKcLV33-11_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS21-BGKcLV33-11_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS21-BGKcLV33-K562	brenton-graveley:RPS21-BGKcLV33-12	brenton-graveley:L-RPS21-BGKcLV33-12	brenton-graveley:RPS21-BGKcLV33-12_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS21-BGKcLV33-12_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR925SFP	ENCBS916YIG	ENCLB608IDU	ENCFF094CUX	ENCFF287BDY	ENCSR816GWS	ENCBS039UVG	ENCLB744ORH	ENCFF537KFS	ENCFF841LQA
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-11	BGKcLV33-12	BGKcLV33-12	BGKcLV33-12	BGKcLV33-12
Sample Name	RPS21-BGKcLV33-11	RPS21-BGKcLV33-11	RPS21-BGKcLV33-11	RPS21-BGKcLV33-11	RPS21-BGKcLV33-11	RPS21-BGKcLV33-11	RPS21-BGKcLV33-12	RPS21-BGKcLV33-12	RPS21-BGKcLV33-12	RPS21-BGKcLV33-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		RPS21-BGKcLV33-11.pdf	L-RPS21-BGKcLV33-11.pdf				RPS21-BGKcLV33-12.pdf	L-RPS21-BGKcLV33-12.pdf
ID	7476	7561	7671	7781	7891	7965	7562	7672	7782	7892

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RPS21-BGKcLV33-11_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2039	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6617
RPS21-BGKcLV33-11_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2039	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6673
RPS21-BGKcLV33-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGKcLV33-11_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18094
RPS21-BGKcLV33-11_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11/Aligned.sortedByCoord.out.bam		ENCORE2	18150
RPS21-BGKcLV33-11_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11/Aligned.sortedByCoord.out.bam		ENCORE2	18206
RPS21-BGKcLV33-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11/Aligned.sortedByCoord.out.bam		ENCORE2	18262
RPS21-BGKcLV33-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11/Aligned.sortedByCoord.out.bam		ENCORE2	18318
RPS21-BGKcLV33-11_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2039					GRCh38	V40	RPS21-BGKcLV33-11_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGKcLV33-11_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18374
RPS21-BGKcLV33-12_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2040	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6618
RPS21-BGKcLV33-12_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2040	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6674
RPS21-BGKcLV33-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGKcLV33-12_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18095
RPS21-BGKcLV33-12_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12/Aligned.sortedByCoord.out.bam		ENCORE2	18151
RPS21-BGKcLV33-12_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12/Aligned.sortedByCoord.out.bam		ENCORE2	18207
RPS21-BGKcLV33-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12/Aligned.sortedByCoord.out.bam		ENCORE2	18263
RPS21-BGKcLV33-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12/Aligned.sortedByCoord.out.bam		ENCORE2	18319
RPS21-BGKcLV33-12_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2040					GRCh38	V40	RPS21-BGKcLV33-12_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGKcLV33-12_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18375